TY - JOUR
T1 - Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model.
AU - Unarta, Ilona Christy
AU - Cao, Siqin
AU - Kubo, Shintaroh
AU - Wang, Wei
AU - Cheung, Peter Pak-Hang
AU - Gao, Xin
AU - Takada, Shoji
AU - Huang, Xuhui
N1 - KAUST Repository Item: Exported on 2021-04-26
Acknowledged KAUST grant number(s): FCC/1/1976-23, FCC/1/1976-26, REI/1/0018-01-01, URF/1/4098-01-01
Acknowledgements: X.H. was supported by the Hong Kong Research Grant Council (16303919, 16307718, AoE/P-705/16, AoE/M-09/12, and T13-605/18-W)
and the Hong Kong Innovation and Technology Commission (ITCPD/17-9 and ITC-CNERC14SC01). X.G. was supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research under Awards FCC/1/1976-23, FCC/1/1976-26, URF/1/4098-01-01, and REI/1/0018-01-01. This research made use of the computing resources of the Supercomputing Laboratory at KAUST and the X-GPU cluster supported by the Hong Kong Research Grant Council Collaborative Research Fund C6021-19EF.
PY - 2021/4/22
Y1 - 2021/4/22
N2 - To initiate transcription, the holoenzyme (RNA polymerase [RNAP] in complex with σ factor) loads the promoter DNA via the flexible
loading gate created by the clamp and β-lobe, yet their roles in DNA loading have not been characterized. We used a quasi-Markov
State Model (qMSM) built from extensive molecular dynamics simulations to elucidate the dynamics of Thermus aquaticus holoenzyme’s gate opening. We showed that during gate opening, β-lobe oscillates four orders of magnitude faster than the clamp, whose opening depends on the Switch 2’s structure. Myxopyronin, an antibiotic that binds to Switch 2, was shown to undergo a conformational selection mechanism to inhibit clamp opening. Importantly, we reveal a critical but undiscovered role of β-lobe, whose opening is sufficient for DNA loading even when the clamp is partially closed. These findings open the opportunity for the development of antibiotics targeting β-lobe of RNAP. Finally, we have shown that our qMSMs, which encode non-Markovian dynamics based on the generalized master equation formalism, hold great potential to be widely applied to study biomolecular dynamics.
AB - To initiate transcription, the holoenzyme (RNA polymerase [RNAP] in complex with σ factor) loads the promoter DNA via the flexible
loading gate created by the clamp and β-lobe, yet their roles in DNA loading have not been characterized. We used a quasi-Markov
State Model (qMSM) built from extensive molecular dynamics simulations to elucidate the dynamics of Thermus aquaticus holoenzyme’s gate opening. We showed that during gate opening, β-lobe oscillates four orders of magnitude faster than the clamp, whose opening depends on the Switch 2’s structure. Myxopyronin, an antibiotic that binds to Switch 2, was shown to undergo a conformational selection mechanism to inhibit clamp opening. Importantly, we reveal a critical but undiscovered role of β-lobe, whose opening is sufficient for DNA loading even when the clamp is partially closed. These findings open the opportunity for the development of antibiotics targeting β-lobe of RNAP. Finally, we have shown that our qMSMs, which encode non-Markovian dynamics based on the generalized master equation formalism, hold great potential to be widely applied to study biomolecular dynamics.
UR - http://hdl.handle.net/10754/668915
UR - http://www.pnas.org/lookup/doi/10.1073/pnas.2024324118
U2 - 10.1073/pnas.2024324118
DO - 10.1073/pnas.2024324118
M3 - Article
C2 - 33883282
SN - 0027-8424
VL - 118
SP - e2024324118
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 17
ER -